Extended Data Fig. 7: Analysis of histone acetylation, and ATAC-seq overview and specific gene loci.
From: Metabolic heterogeneity underlies reciprocal fates of TH17 cell stemness and plasticity
a, ChIP qRT–PCR of pan-acetyl-histone bound to the Ifng promoter of WT or RptorIl17aCre (R26ReYFP) YFP+ cells from dLN (n = 4 per genotype). b, c, WT and RptorIl17aCre (R26ReYFP) mice were immunized with MOG, and YFP+ cells from dLN and spleen at day nine post-immunization were analysed by ATAC-seq. b, Density plot and heat maps of a representative individual ATAC-seq sample, demonstrating separation into different fragment lengths indicative of nucleosome-free, mononucleosome, dinucleosome and trinucleosome patterns, consistent with ref. 15. TSS, transcription start site. c, Correlation plot of nucleosome-free fragments. d, Nucleosome-free ATAC-seq tracks at the Tbx21 and Il12rb2 gene loci, with immediate promoter regions indicated by red boxes. e, Summary of ATAC-seq motif-enrichment data, showing log2 (odds ratio) and log10 (Fisher P-value) of cells from dLN. f, Tn5 insert sites from ATAC-seq analysis of dLN were aligned to motifs for transcription factors from the TRANSFAC database, and the binding profiles of selected transcription factors of the TCF–LEF family are shown. Data are means ± s.e.m. and representative of three independent experiments (a), or from one experiment (b–f). Student’s t-test (two-sided; parametric) was used in panel a to determine statistical significance.
